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Question: TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene name into common gene name
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gravatar for salvocomplicazioni1
12 months ago by
salvocomplicazioni10 wrote:

I'm trying to analyze TCGA RNA-seq data, so i used TCGAbiolinks, I arrived at normalization data step and i obtained normalized counts matrix, How can I change Ensemble gene name into common gene name?

ADD COMMENTlink modified 11 months ago by tiagochst100 • written 12 months ago by salvocomplicazioni10
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gravatar for biomiha
12 months ago by
biomiha10
UK/Cambridge
biomiha10 wrote:

I would use biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html)

ADD COMMENTlink written 12 months ago by biomiha10
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gravatar for tiagochst
11 months ago by
tiagochst100
Brazil
tiagochst100 wrote:

You have the names inside the SummarizedExperiment object.

 

An example is in this gist:

 

For hg38 the gene names are retrieved with

values(data)$external_gene_name

 

For hg19 

values(data)$gene_id

 

Where data is the summarizedExperiment object, this data was created using biomaRt.

ADD COMMENTlink written 11 months ago by tiagochst100
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